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- PDB-2y6n: STRUCTURE OF LINEAR GRAMICIDIN D OBTAINED USING TYPE I CRYSTALS G... -

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Basic information

Entry
Database: PDB / ID: 2y6n
TitleSTRUCTURE OF LINEAR GRAMICIDIN D OBTAINED USING TYPE I CRYSTALS GROWN IN A 8.8 MONOACYLGLYCEROL LIPID CUBIC PHASE.
ComponentsVAL-GRAMICIDIN A
KeywordsANTIBIOTIC / ION CHANNEL / MESOPHASE / SPONGE PHASE
Function / homologyGRAMICIDIN A / O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / :
Function and homology information
Biological speciesBREVIBACILLUS BREVIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsHoefer, N. / Aragao, D. / Caffrey, M.
CitationJournal: Cryst.Growth Des. / Year: 2011
Title: Membrane Protein Crystallization in Lipidic Mesophases. Hosting Lipid Effects on the Crystallization and Structure of a Transmembrane Peptide
Authors: Hoefer, N. / Aragao, D. / Lyons, J. / Caffrey, M.
History
DepositionJan 25, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2013Group: Other
Revision 1.3Jan 15, 2014Group: Database references / Version format compliance
Revision 1.4Mar 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Mar 29, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Category: audit_author / database_2 ...audit_author / database_2 / pdbx_database_status / struct_site
Item: _audit_author.identifier_ORCID / _database_2.pdbx_DOI ..._audit_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VAL-GRAMICIDIN A
B: VAL-GRAMICIDIN A
C: VAL-GRAMICIDIN A
D: VAL-GRAMICIDIN A
E: VAL-GRAMICIDIN A
F: VAL-GRAMICIDIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,20810
Polymers11,2946
Non-polymers4,9144
Water362
1
A: VAL-GRAMICIDIN A
B: VAL-GRAMICIDIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1495
Polymers3,7652
Non-polymers3,3843
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-9.1 kcal/mol
Surface area3980 Å2
MethodPISA
2
C: VAL-GRAMICIDIN A
D: VAL-GRAMICIDIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2943
Polymers3,7652
Non-polymers1,5301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-12.5 kcal/mol
Surface area3080 Å2
MethodPISA
3
E: VAL-GRAMICIDIN A
F: VAL-GRAMICIDIN A


Theoretical massNumber of molelcules
Total (without water)3,7652
Polymers3,7652
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-14.1 kcal/mol
Surface area3010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.616, 62.783, 30.602
Angle α, β, γ (deg.)90.00, 100.02, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.12817, -0.04521, -0.99072), (-0.09705, -0.99474, 0.03284), (-0.98699, 0.09194, -0.13188)-5.10802, -4.60774, -26.03978
2given(-0.99431, 0.09665, 0.04477), (0.09515, 0.99486, -0.03459), (-0.04789, -0.03014, -0.9984)-19.40863, 1.02082, -39.7198

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Components

#1: Protein/peptide
VAL-GRAMICIDIN A / GRAMICIDIN D


Type: Polypeptide / Class: Antibiotic / Mass: 1882.294 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Details: GRAMICIDIN A IS A HEXADECAMERIC HELICAL PEPTIDE WITH ALTERNATING D,L CHARACTERISTICS. THE N-TERM IS FORMYLATED (RESIDUE 0). THE C-TERM IS CAPPED WITH ETHANOLAMINE (RESIDUE 16).
Source: (natural) BREVIBACILLUS BREVIS (bacteria) / References: NOR: NOR00243, GRAMICIDIN A
#2: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#3: Chemical ChemComp-P4C / O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / POLYETHYLENE 400


Mass: 324.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Compound detailsGRAMICIDIN IS A HETEROGENEOUS MIXTURE OF SEVERAL COMPOUNDS INCLUDING GRAMICIDIN A, B AND C WHICH ...GRAMICIDIN IS A HETEROGENEOUS MIXTURE OF SEVERAL COMPOUNDS INCLUDING GRAMICIDIN A, B AND C WHICH ARE OBTAINED FROM BACILLUS BREVIS AND COLLECTIVELY CALLED GRAMICIDIN D HERE, GRAMICIDIN A IS REPRESENTED BY THE SEQUENCE (SEQRES) GROUP: 1 NAME: GRAMICIDIN A CHAIN: A, B, C, D, E. F COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 16 DESCRIPTION: GRAMICIDIN A IS A HEXADECAMERIC HELICAL PEPTIDE WITH ALTERNATING D,L CHARACTERISTICS. THE N-TERM IS FORMYLATED (RESIDUE 1) WITH ETHANOLAMINE AT THE C-TERM (RESIDUE 16)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52 %
Description: DATA WERE COLLECTED USING A COLLIMATED MINIBEAM WITH A 10 MICRON BEAMSIZE
Crystal growMethod: lipidic cubic phase
Details: 30 %(W/V) POLYETHYLENE GLYCOL (PEG) 8000, 0.2 M NH4SO4, LIPIDIC CUBIC PHASE OF 8.8 MAG (SN-1-O-(CIS-8)HEXADECENYLGLYCEROL) WAS USED IN A RATIO OF 1:20 (MOL/MOL) GRAMICIDIN D TO 8.8 MAG.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9795
DetectorType: MARRESEARCH MX-300 / Detector: CCD / Date: Feb 22, 2009 / Details: SI(111) DOUBLE CRYSTAL
RadiationMonochromator: DOUBLE CRYSTAL CRYO-COOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.26→30.15 Å / Num. obs: 28320 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 9.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.6
Reflection shellResolution: 1.26→1.29 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.5 / % possible all: 76.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y5M

2y5m


Resolution: 1.26→30.15 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.027 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE 15P A1016 IN THIS ENTRY WAS NAMED PEG-A IN THE PRIMARY CITATION. RESIDUES 15P A1017 AND 15P A1018 IN THIS ENTRY WERE NAMED PEG-B ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE 15P A1016 IN THIS ENTRY WAS NAMED PEG-A IN THE PRIMARY CITATION. RESIDUES 15P A1017 AND 15P A1018 IN THIS ENTRY WERE NAMED PEG-B AND PEG-B' RESPECTIVELY IN THE PRIMARY CITATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.16983 1536 5.1 %RANDOM
Rwork0.14803 ---
obs0.14917 28320 96.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.441 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å2-0.5 Å2
2--1.77 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 1.26→30.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms816 0 98 2 916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221014
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7751.9481342
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.523592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6042024
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.7631540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1220.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.02592
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1331.5518
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.552780
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.053496
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.7754.5558
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.80431014
X-RAY DIFFRACTIONr_sphericity_free18.26332
X-RAY DIFFRACTIONr_sphericity_bonded12.43972
LS refinement shellResolution: 1.258→1.291 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 94 -
Rwork0.197 1670 -
obs--76.9 %

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